Hi
I had the same issue with page numbering not aligning to the bottom margin. In my example, shown below, the page number is shown in a table with the last paragraph marker below the table. Using a table to align page numbering etc. can be an issue as the paragraph marker stops the page number from aligning correctly to the bottom margin.
Solution: ... highlight the paragraph marker and change the font size to '1' pt. Then set the paragraph spacing to 'Single' and spacing above and below set to '0'.
So in your case, you may or may not have a table but in any case check to see if there's a paragraph marker following the page number. Switch on Show all (in the Paragraph group on the Home tab) and try my solution above.
Best wishes